title: Prediction and characterization of protein-protein interaction network in Xanthomonas oryzae pv. oryzae PXO99 A.
abstract: Xanthomonas oryzae pv. oryzae (Xoo), the causal agent of bacterial blight disease in rice, is one of the most serious plant pathogens worldwide. In the current analysis, we constructed a protein-protein interaction network of Xoo strain PXO99(A) with two computational approaches (interolog method and domain combination method), and verified by K-Nearest Neighbors classification method. The predicted PPI network of Xoo PXO99(A) contains 36,886 interactions among 1988 proteins. KNN verification and GO annotation confirm the reliability of the network. Detailed analysis of flagellar synthesis and chemotaxis system shows that σ factors (especially σ(28), σ(54)) in Xoo PXO99(A) are very important for flagellar synthesis and motility, and transcription factors RpoA, RpoB and RpoC are hubs to connect most σ factors. Furthermore, Xoo PXO99(A) may have both cAMP and c-di-GMP signal transduction system, and the latter is especially important for this plant pathogen. This study therefore provides valuable clues to explore the pathogenicity and metabolic regulation of Xoo PXO99(A).
authors.affiliation: State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China; Center for Bioinformatics, Huazhong Agricultural University, Wuhan 430070, PR China. Electronic address: gj30501@163.com.
authors.forename: Jing
authors.initials: J
authors.lastname: Guo
authors.forename: Huan
authors.initials: H
authors.lastname: Li
authors.forename: Ji-Wei
authors.initials: JW
authors.lastname: Chang
authors.forename: Yang
authors.initials: Y
authors.lastname: Lei
authors.forename: Sen
authors.initials: S
authors.lastname: Li
authors.forename: Ling-Ling
authors.initials: LL
authors.lastname: Chen
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics* / Q000378:metabolism*; D019295:Computational Biology / Q000379:methods; D015964:Gene Expression Regulation, Bacterial; D012275:Oryza / Q000382:microbiology; D010935:Plant Diseases / Q000382:microbiology; D060066:Protein Interaction Maps; D015398:Signal Transduction; D013312:Stress, Physiological; D014974:Xanthomonas / Q000235:genetics* / Q000378:metabolism*
chemical_list: D001426:Bacterial Proteins
keywords: Domain combination method; Flagellar and chemotaxis system; Interolog method; K-nearest neighbors classification method; Signal transduction system